4JUO

A low-resolution three-gate structure of topoisomerase IV from Streptococcus pneumoniae in space group H32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.53 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.

Laponogov, I.Veselkov, D.A.Crevel, I.M.Pan, X.S.Fisher, L.M.Sanderson, M.R.

(2013) Nucleic Acids Res 41: 9911-9923

  • DOI: 10.1093/nar/gkt749
  • Primary Citation of Related Structures:  
    4JUO, 4I3H

  • PubMed Abstract: 
  • Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G- ...

    Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, 3rd floor New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK and Division of Biomedical Sciences, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit A A496Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parCSP_0855
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B C670Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parESP_0852
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    E-site DNAE11N/A
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      E-site DNAF15N/A
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      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        E-site DNAG11N/A
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        • Entity ID: 6
          MoleculeChainsLengthOrganismImage
          E-site DNAH15N/A
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          LFX
          Query on LFX

          Download Ideal Coordinates CCD File 
          F
          (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid
          C18 H20 F N3 O4
          GSDSWSVVBLHKDQ-JTQLQIEISA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          A, C
          MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 6.53 Å
          • R-Value Free: 0.298 
          • R-Value Work: 0.247 
          • R-Value Observed: 0.250 
          • Space Group: H 3 2
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 213.58α = 90
          b = 213.58β = 90
          c = 211.83γ = 120
          Software Package:
          Software NamePurpose
          GDEdata collection
          PHASERphasing
          PHENIXrefinement
          xia2data reduction
          XDSdata reduction
          xia2data scaling
          SCALAdata scaling

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History 

          • Version 1.0: 2013-08-28
            Type: Initial release
          • Version 1.1: 2013-09-04
            Changes: Database references
          • Version 1.2: 2013-12-04
            Changes: Database references
          • Version 1.3: 2017-11-15
            Changes: Refinement description